US 12,331,363 B2
Digital analysis of blood samples to determine efficacy of cancer therapies for specific cancers
Daniel Haber, Chestnut Hill, MA (US); Shyamala Maheswaran, Lexington, MA (US); Tanya Todorova, Malden, MA (US); Mark Kalinich, Cambridge, MA (US); David Tomoaki Miyamoto, Wellesley, MA (US); and Xin Hong, Malden, MA (US)
Assigned to The General Hospital Corporation, Boston, MA (US)
Filed by The General Hospital Corporation, Boston, MA (US)
Filed on May 27, 2022, as Appl. No. 17/826,834.
Application 17/826,834 is a division of application No. 16/344,557, granted, now 11,371,101, previously published as PCT/US2017/058855, filed on Oct. 27, 2017.
Claims priority of provisional application 62/413,952, filed on Oct. 27, 2016.
Prior Publication US 2022/0364185 A1, Nov. 17, 2022
Int. Cl. C12Q 1/6886 (2018.01)
CPC C12Q 1/6886 (2013.01) [C12Q 2600/158 (2013.01)] 15 Claims
 
1. A method for determining whether a subject diagnosed with prostate cancer will improve if treated only with an anti-androgenic treatment regimen, the method comprising
isolating circulating tumor cells (CTCs) from a blood sample from the subject before treatment with an anti-androgenic treatment regimen begins;
converting CTC-derived RNA into cDNA molecules in a cDNA-containing solution;
encapsulating the cDNA molecules into individual droplets;
amplifying the cDNA molecules in each droplet using probes and primers specific for cDNA molecules within each of the droplets that correspond to FOLH1 (PSMA) and HOXB13 genes in the presence of a reporter group bound to a nucleic acid configured to bind specifically to cDNA molecules that correspond to FOLH1 (PSMA) and HOXB13 genes from CTCs and not to cDNA molecules from other cells in the blood; and
determining a presence and expression level of FOLH1 (PSMA) and HOXB13 genes in the CTCs in the blood sample,
wherein expression levels of the FOLH1 (PSMA) and HOXB13 genes determined in the CTCs in the blood sample that are both elevated above a background noise level as determined by evaluation of healthy donors without prostate cancer indicate that the subject will not improve if treated only with an anti-androgenic treatment regimen.